GlyPID 2.0, a software tool for accurate characterization of protein glycosylation through a combination of the following techniques.
Accurate precursor ion mass calculated using THRASH–based deisotoping methods
A CID score calculated from Collision-Induced Dissociation (CID) spectra, similar to previous version of GlypID [1]. The model is based on spacing between fragment peaks indicative of glycan fragmentation.
A new HCD score calculated from High-energy C-trap Dissociation (HCD) spectra scoring technique based on the presence of characterestic glycan peaks. HCD is available on the LTQ Orbitrap XL.
[1]Mayampurath et. al., DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra. Bioinformatics. 2008 Apr 1;24(7):1021-3
[2]Horn, et. al. Automated Reduction and Interpretation of High Resolution Electrospray Mass Spectra of Large Molecules. J. Am. Soc. Mass Spectrom. 2000, 11, 320-332.
[3]Wu et. al. A Comp. Approach for the Identification of Site-Specific Protein Glycosylations Through Ion-Trap Mass Spectrometry, Lecture Notes in Comp Sci, 2007, 4532:96-107.
MultiGlycan helps user to gather glycan profile information from LC-MS Spectra. It also reports quantity of specific glycan composition. We've developed two different versions of MultiGlycan: one for MALDI, and the other one for ESI. The MALDI version deconvolutes regular and overlapping glycans using simple model matching; The ESI version extracts glycans using adduct information.
"Automated Annotation and Quantification of Glycans Using Liquid Chromatography Mass Spectrometry (LC-MS)." Bioinformatics, C.Y. Yu, A. Mayampurath, Y. Hu, Y. Mechref and H. Tang, Apr 2013 ==
GlycoFragwork: GlycoFragwork analyzes multiple pre-aligned LC-MS/MS datasets, and reports a list (termed as a 'glycomap') of identified intact glycopeptides with their mass, elution time and abundance[link]
CStat: Computational methods for biomarker discovery in proteomics and glycomics [link]
LipidAT: Automated analysis of lipidomic mass spectrometry data[link]
GlyPID: N-glycosylation peptide identification tool[link]
GlyPID 2.0, a software tool for accurate characterization of protein glycosylation through a combination of the following techniques.
[1]Mayampurath et. al., DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra. Bioinformatics. 2008 Apr 1;24(7):1021-3
[2]Horn, et. al. Automated Reduction and Interpretation of High Resolution Electrospray Mass Spectra of Large Molecules. J. Am. Soc. Mass Spectrom. 2000, 11, 320-332.
[3]Wu et. al. A Comp. Approach for the Identification of Site-Specific Protein Glycosylations Through Ion-Trap Mass Spectrometry, Lecture Notes in Comp Sci, 2007, 4532:96-107.
MultiGlycan: Glycan profiling tool (MALDI/LC-ESI)[link]
GlycoFragwork: GlycoFragwork analyzes multiple pre-aligned LC-MS/MS datasets, and reports a list (termed as a 'glycomap') of identified intact glycopeptides with their mass, elution time and abundance[link]
GlycanSeq: Glycopeptide sequencing tool[link]